Imported .FBX file from fusion opens with multiple dotted lines and empties, I can't remove them without changing the objects' allignments
The dotted lines are relationship lines. They mean that one of the object is the parent of the other, which in turns means that if you transform (move, rotate, scale) the parent object, all its child objects will have the same transformation applied.
You can "unparent" objects by selecting them and then using either :


The shorcut ALT + P then choosing "Clear and keep transformations"
Object (top or bottom bar of you 3d view) > Parent > "Clear and keep transformations"


Then, the relation lines should disappear and you can freely delete your empties.

I would advise selecting ALL your objects in the scene and unparenting them all at once while keeping their transform.